Chapter 3 Physical and Biological Resources 3.1 Introduction This chapter presents the physical and biological setting of the HCP/NCCP inventory area. It describes the baseline physical and biological conditions upon which the impact analyses (Chapter 4) and conservation strategy (Chapter 5) are based. The chapter describes how existing and new data were collected to create the baseline inventory. The setting of the inventory area is described in the context of the subject areas listed below. Physical resources. Existing land-cover types. Historic conditions. Natural communities. Wetlands, streams, and other jurisdictional waters. Covered species. Biological resources have been considered at several scales (i.e., the regional landscape, watershed, subwatershed, habitat, and species level) to address the regulatory requirements of ESA, CESA, NCCPA, Section 404 of the CWA, and Section 1601 of the California Fish and Game Code. These scales are not mutually exclusive; for example, many wetlands and streams are also habitat for covered species, and many ecosystem functions support biological diversity and habitat for covered species. 3.2 Data Collection 3.2.1 Physical Features Sources used to map and describe the physical setting of the inventory area included U.S. Geological Survey (USGS) data on topography and hydrology; geologic maps of the area (California Department of Conservation 1990; U.S. Geological Survey 1994); soil survey information (Soil Conservation Service East Contra Costa County HCP/NCCP DRAFT June 2005 3-1 01478.01 East Contra Costa County Chapter 3 Habitat Conservation Plan Association Physical and Biological Resources 1977); and other published information (Hickman 1993; Alt and Hyndman 2000). Topography, hydrology, and soil data were downloaded from agency web sites and imported into ArcInfo, where files were clipped and converted into the projection for the inventory area. 3.2.2 Land-Cover Mapping One of the primary data sources for this Plan is a detailed GIS-based map of land-cover types within the inventory area (see below for data sources). Land- cover type is defined as the dominant character of the land surface discernible from aerial photographs, as determined by vegetation, water, or human uses. Land-cover types are the most widely used units in analyzing ecosystem function, habitat diversity, covered natural communities, wetlands and streams, and covered species habitat. Data sources, mapping standards, and the classification and interpretation of land-cover types are discussed below. Data Sources The primary sources of information for the land-cover mapping in the inventory area were: orthorectified black-and-white aerial photographs (provided by Contra Costa County; flown in May 2000) for the entire inventory area (scale in rural areas is 1 inch = 400 feet; scale in urban areas is 1 inch = 200 feet); color infrared photographs (scale 1:6,000) taken in June 1987 and 1988; covered inventory area except southeastern corner (provided by Contra Costa Water District); National Wetlands Inventory Maps (scale 1:65,000) based on color-infrared photographs taken in 1985; USGS streams, wetlands, and roads data (USGS digital line graph data— various dates); Detailed stream data from the Contra Costa watershed atlas (Contra Costa County 2003); and California Department of Water Resources Land Use Data (1995). The ancillary data sources listed below were used to obtain information not available in the primary sources and to check the mapped information for accuracy. East Alameda–Contra Costa Biodiversity Study (Conservation opportunity mapping in eastern Contra Costa County) (Jones & Stokes Associates 1996). Habitat mapping within the Los Vaqueros Reservoir watershed (Jones & Stokes Associates 1994). East Contra Costa County HCP/NCCP DRAFT June 2005 3-2 01478.01 East Contra Costa County Chapter 3 Habitat Conservation Plan Association Physical and Biological Resources Color aerial photographs (scale 1:6000) taken in February 1987; covered southeastern corner of inventory area (Jones & Stokes file data). Soil survey mapping (Soil Conservation Service 1977). Vegetation maps of CCWD interim service area (Contra Costa Water District 2000). Geologic maps of the San Francisco–San Jose Quadrangle (California Department of Conservation 1990). Draft Environmental Impact Report for the Cowell Ranch Project General Plan Amendment and Related Actions (Contra Costa County 1996a). Recent delineations of jurisdictional wetlands verified by USACE within the inventory area (e.g., Darwin Myers Associates 2003, U.S. Army Corps of Engineers 2003). Current residential development maps (provided by Contra Costa County). Personal communications with knowledgeable specialists (Chapter 12). In addition to using existing data sets, Jones & Stokes biologists conducted field visits. An initial field visit was conducted on December 7, 2001, to develop the land-cover classification and to perform preliminary verification of aerial photograph signatures. Two other field visits, on January 10 and May 26, 2002, were conducted to verify land-cover types and consistency of mapping and to collect additional data for land-cover type descriptions. Initial mapping was verified by visual inspection from locations accessible by public roads. Areas were selected for field verification on the basis of the land-cover types present and the accessibility of the area. Once field visits were conducted, land-cover mapping was revised on the basis of field findings. Comments of the HCP/NCCP Scientific Advisory Panel on the draft land-cover maps indicated the need for follow-up field surveys to increase the accuracy of the data set. In particular, the panel identified the need to collect data on the occurrence and extent of “small-scale features,” such as rock outcrops, caves, serpentine areas, small ponds, and vernal pools, that may have been missed during the initial mapping effort. Field surveys were also recommended to increase the accuracy of mapped locations of alkali grasslands and wetlands and to update the mapping from the 2000 air photos. These intensive follow-up field surveys were conducted on April 29, April 30, May 1, and May 13, 2003. Mapping Procedures Land-cover types were mapped onto hard copies of the black-and-white photographs (scale 1 inch = 400 feet) by using the available signatures and supplementing them with information derived from the other primary sources discussed above as appropriate. A 10-acre minimum mapping unit was used for all land-cover types, except for riparian, wetland, wind turbine, and rock outcrop land-cover types; these features were originally mapped in 2001 with a 1-acre East Contra Costa County HCP/NCCP DRAFT June 2005 3-3 01478.01 East Contra Costa County Chapter 3 Habitat Conservation Plan Association Physical and Biological Resources minimum mapping unit. These features were revised during the small-scale features mapping in spring 2003 and were mapped to the smallest scale possible (<0.25 acre) using the 2000 air photos and extensive field surveys where sites could be accessed from public roads (see additional methods described below). Maps were digitized using AutoCad Release 14. Following the completion of all digitizing, the AutoCad file was converted to a GIS coverage using ArcInfo. ArcInfo was used to edit the coverage and calculate acreage for each land-cover type. The final hard copies of the land-cover maps were then produced using ArcMap. Ancillary information was used to supplement land-cover information acquired by aerial photograph interpretation. Color aerial photographs (February 1987) were used to spot check signatures in areas not covered by the infrared photographs. Soil Conservation Service (SCS) soils maps were used to identify areas with alkaline soils (Soil Conservation Service 1977). Streams in the inventory area were mapped by staff of the Contra Costa County Community Development and Public Works Departments. Mapping was done County-wide to support the concurrent development of a County watershed atlas (Contra Costa County 2003). See the description of the stream land cover type below for more details on mapping methods. Land use maps, permitted development maps, and interviews with city and County staff were used to further refine agricultural and urban land-cover types. Mapped signatures for specific land-cover types were also compared with field- verified maps prepared for the Los Vaqueros reservoir project (Jones & Stokes Associates 1996) and for large projects in the inventory area (e.g., Contra Costa County 1996a; Mundie & Associates and City of Antioch 2002) to verify the accuracy of the current mapping effort. If the land-cover type was not easily identifiable to the lowest classification level from the photographs or other available information, it was mapped at the higher classification level. Wetlands that could not be classified by type (seasonal or otherwise), for example, were mapped at the highest classification level (i.e., wetlands). Wetland mapping was compared with recent wetland delineations verified by the USACE (Darwin Myers Associates 2003; USACE 2003) to further refine photointerpretation methods. Jones & Stokes biologists conducted extensive field surveys of the inventory area over 4 days between April 29 and May 13, 2003; February 17, 2004; and over 4 days between May 5 and June 2, 2004. The surveys were designed to substantially improve the original land-cover data set by accomplishing the objectives listed below. Updating the land-cover